This tool is used to compare GTF files with a reference GTF. Currently it generates 6 files for each query GTF as follows:
| File Name | File Extension | Description |
|---|---|---|
| <query GTF> | exon | Reports the best match (if found) for each exon found in the query GTF |
| itracking | Reports the query GTF interval structure and it's overlap with reference GTF if found | |
| tstat | Temporary simple statistics file on the query GTF to be used later within the tool | |
| <ref_query GTF> | exon | Reports the best match (if found) for each exon found in the reference GTF |
| itracking | Reports the reference GTF interval structure and it's overlap with the query GTF if found | |
| ref | tstat | Temporary simple statistics file on the reference GTF to be used later within the tool |
# Install pypy
sudo apt install pypy
# Download pip
wget https://bootstrap.pypa.io/get-pip.py
pypy get-pip.py
# Install intervaltree
pypy -m pip install intervaltree
pypy -m pip install numpy
git clone https://github.com/abdelrahmanMA/gtf-compare.git
cd gtf-compare/gtfcompare
pypy compare.py -r [<reference.gtf>] [<query.gtf> [<query.gtf> ...]]
You can pass as many query GTFs as you want. Alternatively -i can be used to pass a text file with a list of query GTFs
pypy compare.py -r [<reference.gtf>] -i [<list.txt>]
This tool can be used with python 2.7 and python 3.6, but for the sake of speed pypy is recommended.